Question

I have two tables that I’m filling, ‘msrun’ and ‘feature’. ‘feature’ has a foreign key pointing to the ‘msrun_name’ column of the ‘msrun’ table. Inserting in the tables works fine. But when I try to delete from the ‘feature’ table I get the following error:

pysqlite2.dbapi2.OperationalError: foreign key mismatch

From the rules of foreign keys in the manual of SQLite:

- The parent table does not exist, or
- The parent key columns named in the foreign key constraint do not exist, or
- The parent key columns named in the foreign key constraint are not the primary key of the parent table and are not subject to a unique constraint using collating sequence specified in the CREATE TABLE, or
- The child table references the primary key of the parent without specifying the primary key columns and the number of primary key columns in the parent do not match the number of child key columns.

I can see nothing that I’m violating. My create tables look like this:

DROP TABLE IF EXISTS `msrun`;
-- -----------------------------------------------------
-- Table `msrun`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `msrun` (
  `msrun_name` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `description` VARCHAR(500) NOT NULL );

DROP TABLE IF EXISTS `feature`;
-- -----------------------------------------------------
-- Table `feature`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature` (
  `feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `intensity` DOUBLE NOT NULL ,
  `overallquality` DOUBLE NOT NULL ,
  `charge` INT NOT NULL ,
  `content` VARCHAR(45) NOT NULL ,
  `msrun_msrun_name` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_feature_msrun1`
    FOREIGN KEY (`msrun_msrun_name` )
    REFERENCES `msrun` (`msrun_name` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE UNIQUE INDEX `id_UNIQUE` ON `feature` (`feature_id` ASC);
  CREATE INDEX `fk_feature_msrun1` ON `feature` (`msrun_msrun_name` ASC);

As far as I can see the parent table exists, the foreign key is pointing to the right parent key, the parent key is a primary key and the foreign key specifies the primary key column.

The script that produces the error:

from pysqlite2 import dbapi2 as sqlite
import parseFeatureXML


connection = sqlite.connect('example.db')
cursor = connection.cursor()    
cursor.execute("PRAGMA foreign_keys=ON")

inputValues = ('example', 'description')
cursor.execute("INSERT INTO `msrun` VALUES(?, ?)", inputValues)
featureXML = parseFeatureXML.Reader('../example_scripts/example_files/input/featureXML_example.featureXML')

for feature in featureXML.getSimpleFeatureInfo():
    inputValues = (featureXML['id'], featureXML['intensity'],
                   featureXML['overallquality'], featureXML['charge'], 
                   featureXML['content'], 'example')
    # insert the values into msrun using ? for sql injection safety
    cursor.execute("INSERT INTO `feature` VALUES(?,?,?,?,?,?)", inputValues)
connection.commit()

for feature in featureXML.getSimpleFeatureInfo():
    cursor.execute("DELETE FROM `feature` WHERE feature_id = ?", (str(featureXML['id']),))    

---

Edit:

These are the tables that have foreign keys linking to features. They are not being filled yet:

DROP TABLE IF EXISTS `convexhull`;
-- -----------------------------------------------------
-- Table `convexhull`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `convexhull` (
  `convexhull_id` INT PRIMARY KEY NOT NULL ,
  `mz` DOUBLE NOT NULL ,
  `rt` DOUBLE NOT NULL ,
  `feature_feature_id` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_convexhull_feature`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_convexhull_feature` ON `convexhull` (`feature_feature_id` ASC);

DROP TABLE IF EXISTS `position`;
-- -----------------------------------------------------
-- Table `position`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `position` (
  `position_id` INT PRIMARY KEY NOT NULL ,
  `dim0` INT NOT NULL ,
  `dim1` INT NOT NULL ,
  `feature_feature_id` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_position_feature1`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_position_feature1` ON `position` (`feature_feature_id` ASC);

DROP TABLE IF EXISTS `userParam_names`;
-- -----------------------------------------------------
-- Table `userParam_names`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `userParam_names` (
  `userParam_id` INT PRIMARY KEY NOT NULL ,
  `Name` VARCHAR(45) NOT NULL );

DROP TABLE IF EXISTS `feature_has_userParam_names`;
-- -----------------------------------------------------
-- Table IF EXISTS `feature_has_userParam_names`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature_has_userParam_names` (
  `feature_feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `userParam_names_userParam_id` INT NOT NULL ,
  CONSTRAINT `fk_feature_has_userParam_names_feature1`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_feature_has_userParam_names_userParam_names1`
    FOREIGN KEY (`userParam_names_userParam_id` )
    REFERENCES `userParam_names` (`userParam_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_feature_has_userParam_names_userParam_names1` ON `feature_has_userParam_names` (`userParam_names_userParam_id` ASC);
  CREATE INDEX `fk_feature_has_userParam_names_feature1` ON `feature_has_userParam_names` (`feature_feature_id` ASC);

DROP TABLE IF EXISTS `userParam_value`;
-- -----------------------------------------------------
-- Table IF EXISTS `userParam_value`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `userParam_value` (
  `iduserParam_value` INT PRIMARY KEY NOT NULL ,
  `userParam_name` VARCHAR(45) NOT NULL ,
  `value` VARCHAR(45) NOT NULL );

DROP TABLE IF EXISTS `feature_has_userParam_names_has_userParam_value`;
-- -----------------------------------------------------
-- Table `feature_has_userParam_names_has_userParam_value`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature_has_userParam_names_has_userParam_value` (
  `feature_has_userParam_names_feature_feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `feature_has_userParam_names_userParam_names_userParam_id` INT NOT NULL ,
  `userParam_value_iduserParam_value` INT NOT NULL ,
  CONSTRAINT `fk_feature_has_userParam_names_has_userParam_value_feature_ha1`
    FOREIGN KEY (`feature_has_userParam_names_feature_feature_id` , `feature_has_userParam_names_userParam_names_userParam_id` )
    REFERENCES `feature_has_userParam_names` (`feature_feature_id` , `userParam_names_userParam_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_feature_has_userParam_names_has_userParam_value_userParam_1`
    FOREIGN KEY (`userParam_value_iduserParam_value` )
    REFERENCES `userParam_value` (`iduserParam_value` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_feature_has_userParam_names_has_userParam_value_userParam_1` ON  `feature_has_userParam_names_has_userParam_value` (`userParam_value_iduserParam_value` ASC);
  CREATE INDEX `fk_feature_has_userParam_names_has_userParam_value_feature_ha1` ON  `feature_has_userParam_names_has_userParam_value` (`feature_has_userParam_names_feature_feature_id` ASC, `feature_has_userParam_names_userParam_names_userParam_id` ASC);

The delete statement does work when I do it from SQLite manager.

---

edit 2:

Full traceback:

Traceback (most recent call last):
  File "/homes/ndeklein/workspace/MS/Trunk/PyMS_dev/database/test.py", line 25, in <module>
    cursor.execute("DELETE FROM `feature` WHERE feature_id = 'f_13020522388175237334'")
pysqlite2.dbapi2.OperationalError: foreign key mismatch

Doing

DELETE FROM `feature` WHERE feature_id = 'f_13020522388175237334'

in SQLite Manager works.

---

Edit 3

Including all tables:

--------------------------------------------------------
-- pyMS database. Drops all tables before it makes them, should be changed before release
--------------------------------------------------------


DROP TABLE IF EXISTS `msrun`;
-- -----------------------------------------------------
-- Table `msrun`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `msrun` (
  `msrun_name` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `description` VARCHAR(500) NOT NULL );


DROP TABLE IF EXISTS `feature`;
-- -----------------------------------------------------
-- Table `feature`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature` (
  `feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `intensity` DOUBLE NOT NULL ,
  `overallquality` DOUBLE NOT NULL ,
  `charge` INT NOT NULL ,
  `content` VARCHAR(45) NOT NULL ,
  `msrun_msrun_name` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_feature_msrun1`
    FOREIGN KEY (`msrun_msrun_name` )
    REFERENCES `msrun` (`msrun_name` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE UNIQUE INDEX `id_UNIQUE` ON `feature` (`feature_id` ASC);
  CREATE INDEX `fk_feature_msrun1` ON `feature` (`msrun_msrun_name` ASC);


DROP TABLE IF EXISTS `convexhull`;
-- -----------------------------------------------------
-- Table `convexhull`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `convexhull` (
  `convexhull_id` INT PRIMARY KEY NOT NULL ,
  `mz` DOUBLE NOT NULL ,
  `rt` DOUBLE NOT NULL ,
  `feature_feature_id` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_convexhull_feature`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_convexhull_feature` ON `convexhull` (`feature_feature_id` ASC);


DROP TABLE IF EXISTS `position`;
-- -----------------------------------------------------
-- Table `position`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `position` (
  `position_id` INT PRIMARY KEY NOT NULL ,
  `dim0` INT NOT NULL ,
  `dim1` INT NOT NULL ,
  `feature_feature_id` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_position_feature1`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_position_feature1` ON `position` (`feature_feature_id` ASC);


DROP TABLE IF EXISTS `userParam_names`;
-- -----------------------------------------------------
-- Table `userParam_names`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `userParam_names` (
  `userParam_id` INT PRIMARY KEY NOT NULL ,
  `Name` VARCHAR(45) NOT NULL );


DROP TABLE IF EXISTS `feature_has_userParam_names`;
-- -----------------------------------------------------
-- Table IF EXISTS `feature_has_userParam_names`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature_has_userParam_names` (
  `feature_feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `userParam_names_userParam_id` INT NOT NULL ,
  CONSTRAINT `fk_feature_has_userParam_names_feature1`
    FOREIGN KEY (`feature_feature_id` )
    REFERENCES `feature` (`feature_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_feature_has_userParam_names_userParam_names1`
    FOREIGN KEY (`userParam_names_userParam_id` )
    REFERENCES `userParam_names` (`userParam_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_feature_has_userParam_names_userParam_names1` ON `feature_has_userParam_names` (`userParam_names_userParam_id` ASC);
  CREATE INDEX `fk_feature_has_userParam_names_feature1` ON `feature_has_userParam_names` (`feature_feature_id` ASC);


DROP TABLE IF EXISTS `userParam_value`;
-- -----------------------------------------------------
-- Table IF EXISTS `userParam_value`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `userParam_value` (
  `iduserParam_value` INT PRIMARY KEY NOT NULL ,
  `userParam_name` VARCHAR(45) NOT NULL ,
  `value` VARCHAR(45) NOT NULL );


DROP TABLE IF EXISTS `feature_has_userParam_names_has_userParam_value`;
-- -----------------------------------------------------
-- Table `feature_has_userParam_names_has_userParam_value`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `feature_has_userParam_names_has_userParam_value` (
  `feature_has_userParam_names_feature_feature_id` VARCHAR(40) PRIMARY KEY NOT NULL ,
  `feature_has_userParam_names_userParam_names_userParam_id` INT NOT NULL ,
  `userParam_value_iduserParam_value` INT NOT NULL ,
  CONSTRAINT `fk_feature_has_userParam_names_has_userParam_value_feature_ha1`
    FOREIGN KEY (`feature_has_userParam_names_feature_feature_id` , `feature_has_userParam_names_userParam_names_userParam_id` )
    REFERENCES `feature_has_userParam_names` (`feature_feature_id` , `userParam_names_userParam_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_feature_has_userParam_names_has_userParam_value_userParam_1`
    FOREIGN KEY (`userParam_value_iduserParam_value` )
    REFERENCES `userParam_value` (`iduserParam_value` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_feature_has_userParam_names_has_userParam_value_userParam_1` ON  `feature_has_userParam_names_has_userParam_value` (`userParam_value_iduserParam_value` ASC);
  CREATE INDEX `fk_feature_has_userParam_names_has_userParam_value_feature_ha1` ON  `feature_has_userParam_names_has_userParam_value` (`feature_has_userParam_names_feature_feature_id` ASC, `feature_has_userParam_names_userParam_names_userParam_id` ASC);


DROP TABLE IF EXISTS `precursor`;
-- -----------------------------------------------------
-- Table `precursor`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `precursor` (
  `precursor_id` INT PRIMARY KEY NOT NULL ,
  `ion_mz` DOUBLE NOT NULL ,
  `charge_state` INT NOT NULL ,
  `peak_intensity` DOUBLE NOT NULL );


DROP TABLE IF EXISTS `spectrum`;
-- -----------------------------------------------------
-- Table `spectrum`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `spectrum` (
  `spectrum_index` INT PRIMARY KEY NOT NULL ,
  `ms_level` INT NOT NULL ,
  `base_peak_mz` DOUBLE NOT NULL ,
  `base_peak_intensity` DOUBLE NOT NULL ,
  `total_ion_current` DOUBLE NOT NULL ,
  `lowest_observes_mz` DOUBLE NOT NULL ,
  `highest_observed_mz` DOUBLE NOT NULL ,
  `scan_start_time` DOUBLE NOT NULL ,
  `ion_injection_time` DOUBLE NOT NULL ,
  `msrun_msrun_name` VARCHAR(40) NOT NULL ,
  `precursor_precursor_id` INT NOT NULL ,
  CONSTRAINT `fk_spectrum_msrun1`
    FOREIGN KEY (`msrun_msrun_name` )
    REFERENCES `msrun` (`msrun_name` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_spectrum_precursor1`
    FOREIGN KEY (`precursor_precursor_id` )
    REFERENCES `precursor` (`precursor_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_spectrum_msrun1` ON `spectrum` (`msrun_msrun_name` ASC);
  CREATE INDEX `fk_spectrum_precursor1` ON `spectrum` (`precursor_precursor_id` ASC);


DROP TABLE IF EXISTS `spectrum_has_feature`;
-- -----------------------------------------------------
-- Table `spectrum_has_feature`
-- -----------------------------------------------------
CREATE  TABLE IF NOT EXISTS `spectrum_has_feature` (
  `spectrum_spectrum_index` INT PRIMARY KEY NOT NULL ,
  `spectrum_msrun_msrun_name` VARCHAR(40) NOT NULL ,
  `spectrum_precursor_precursor_id` INT NOT NULL ,
  `feature_feature_id` VARCHAR(40) NOT NULL ,
  `feature_msrun_msrun_name` VARCHAR(40) NOT NULL ,
  CONSTRAINT `fk_spectrum_has_feature_spectrum1`
    FOREIGN KEY (`spectrum_spectrum_index` , `spectrum_msrun_msrun_name` , `spectrum_precursor_precursor_id` )
    REFERENCES `spectrum` (`spectrum_index` , `msrun_msrun_msrun_name` , `precursor_precursor_id` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT `fk_spectrum_has_feature_feature1`
    FOREIGN KEY (`feature_feature_id` , `feature_msrun_msrun_name` )
    REFERENCES `feature` (`feature_id` , `msrun_msrun_msrun_name` )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX `fk_spectrum_has_feature_feature1` ON `spectrum_has_feature` (`feature_feature_id` ASC, `feature_msrun_msrun_name` ASC);
  CREATE INDEX `fk_spectrum_has_feature_spectrum1` ON `spectrum_has_feature` (`spectrum_spectrum_index` ASC, `spectrum_msrun_msrun_name` ASC, `spectrum_precursor_precursor_id` ASC);

Answer 1

You mention that it works in SQLite Manager. I am also unable to reproduce so I’m wondering if there is either an issue with the version of pysqlite2 (or its sqlite version), or some side effect from somewhere else in your code.

Can you post the version of pysqlite2 and its sqlite? This is how I do it:

>>> from pysqlite2 import dbapi2 as sqlite
>>> sqlite.version
'2.3.5'
>>> sqlite.sqlite_version
'3.7.7.1'

UPDATE

Can you run this program and let me know if you get the error still?

#!/usr/bin/python
from pysqlite2 import dbapi2 as sqlite

conn = sqlite.connect(':memory:')
cu = conn.cursor()
cu.executescript("""
DROP TABLE IF EXISTS msrun;
CREATE  TABLE IF NOT EXISTS msrun (
  msrun_name VARCHAR(40) PRIMARY KEY NOT NULL ,
  description VARCHAR(500) NOT NULL );

DROP TABLE IF EXISTS feature;
CREATE  TABLE IF NOT EXISTS feature (
  feature_id VARCHAR(40) PRIMARY KEY NOT NULL ,
  msrun_msrun_name VARCHAR(40) NOT NULL ,
  CONSTRAINT fk_feature_msrun1
    FOREIGN KEY (msrun_msrun_name )
    REFERENCES msrun (msrun_name )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE UNIQUE INDEX id_UNIQUE ON feature (feature_id ASC);
  CREATE INDEX fk_feature_msrun1 ON feature (msrun_msrun_name ASC);

DROP TABLE IF EXISTS convexhull;
CREATE  TABLE IF NOT EXISTS convexhull (
  convexhull_id INT PRIMARY KEY NOT NULL ,
  mz DOUBLE NOT NULL ,
  rt DOUBLE NOT NULL ,
  feature_feature_id VARCHAR(40) NOT NULL ,
  CONSTRAINT fk_convexhull_feature
    FOREIGN KEY (feature_feature_id )
    REFERENCES feature (feature_id )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX fk_convexhull_feature ON convexhull (feature_feature_id ASC);

DROP TABLE IF EXISTS position;
CREATE  TABLE IF NOT EXISTS position (
  position_id INT PRIMARY KEY NOT NULL ,
  dim0 INT NOT NULL ,
  dim1 INT NOT NULL ,
  feature_feature_id VARCHAR(40) NOT NULL ,
  CONSTRAINT fk_position_feature1
    FOREIGN KEY (feature_feature_id )
    REFERENCES feature (feature_id )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX fk_position_feature1 ON position (feature_feature_id ASC);

DROP TABLE IF EXISTS userParam_names;
CREATE  TABLE IF NOT EXISTS userParam_names (
  userParam_id INT PRIMARY KEY NOT NULL ,
  Name VARCHAR(45) NOT NULL );

DROP TABLE IF EXISTS feature_has_userParam_names;
CREATE  TABLE IF NOT EXISTS feature_has_userParam_names (
  feature_feature_id VARCHAR(40) PRIMARY KEY NOT NULL ,
  userParam_names_userParam_id INT NOT NULL ,
  CONSTRAINT fk_feature_has_userParam_names_feature1
    FOREIGN KEY (feature_feature_id )
    REFERENCES feature (feature_id )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT fk_feature_has_userParam_names_userParam_names1
    FOREIGN KEY (userParam_names_userParam_id )
    REFERENCES userParam_names (userParam_id )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX fk_feature_has_userParam_names_userParam_names1 ON feature_has_userParam_names (userParam_names_userParam_id ASC);
  CREATE INDEX fk_feature_has_userParam_names_feature1 ON feature_has_userParam_names (feature_feature_id ASC);

DROP TABLE IF EXISTS userParam_value;
CREATE  TABLE IF NOT EXISTS userParam_value (
  iduserParam_value INT PRIMARY KEY NOT NULL ,
  userParam_name VARCHAR(45) NOT NULL ,
  value VARCHAR(45) NOT NULL );

DROP TABLE IF EXISTS feature_has_userParam_names_has_userParam_value;
CREATE  TABLE IF NOT EXISTS feature_has_userParam_names_has_userParam_value (
  feature_has_userParam_names_feature_feature_id VARCHAR(40) PRIMARY KEY NOT NULL ,
  feature_has_userParam_names_userParam_names_userParam_id INT NOT NULL ,
  userParam_value_iduserParam_value INT NOT NULL ,
  CONSTRAINT fk_feature_has_userParam_names_has_userParam_value_feature_ha1
    FOREIGN KEY (feature_has_userParam_names_feature_feature_id , feature_has_userParam_names_userParam_names_userParam_id )
    REFERENCES feature_has_userParam_names (feature_feature_id , userParam_names_userParam_id )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION,
  CONSTRAINT fk_feature_has_userParam_names_has_userParam_value_userParam_1
    FOREIGN KEY (userParam_value_iduserParam_value )
    REFERENCES userParam_value (iduserParam_value )
    ON DELETE NO ACTION
    ON UPDATE NO ACTION);

  CREATE INDEX fk_feature_has_userParam_names_has_userParam_value_userParam_1 ON  feature_has_userParam_names_has_userParam_value (userParam_value_iduserParam_value ASC);
  CREATE INDEX fk_feature_has_userParam_names_has_userParam_value_feature_ha1 ON  feature_has_userParam_names_has_userParam_value (feature_has_userParam_names_feature_feature_id ASC, feature_has_userParam_names_userParam_names_userParam_id ASC);
""")

conn.commit()
cu.execute("PRAGMA foreign_keys=ON")
cu.execute("INSERT INTO msrun VALUES (?,?)", ('bar', 'bar'))
cu.execute("INSERT INTO feature VALUES (?,?)", ('foo','bar'))
cu.execute("INSERT INTO feature VALUES (?,?)", ('foo1','bar'))
conn.commit()

cu.execute("SELECT * FROM feature")
print(cu.fetchall())

cu.execute("DELETE FROM feature WHERE feature_id=?", ("foo", ))
cu.execute("DELETE FROM feature WHERE feature_id=?", (str("foo1"), ))
conn.commit()

cu.execute("SELECT * FROM feature")
print(cu.fetchall())

UPDATE 2

The fact that you did not get some error should rule out that there is any issue with the features table and its dependencies as per the schema you posted. As per the sqlite docs, I’m now assuming you have some other foreign key from/to any descendant/ascendant of the features table that you did not include (e.g. some table you did not mention that depends on some table you mentioned that depends on features).

Here is the part of the sqlite doc on foreign keys that make me believe that:

If the database schema contains foreign key errors that require
looking at more than one table definition to identify, then those
errors are not detected when the tables are created. Instead, such
errors prevent the application from preparing SQL statements that
modify the content of the child or parent tables in ways that use the
foreign keys. Errors reported when content is changed are “DML errors”
and errors reported when the schema is changed are “DDL errors”. So,
in other words, misconfigured foreign key constraints that require
looking at both the child and parent are DML errors. The English
language error message for foreign key DML errors is usually “foreign
key mismatch” but can also be “no such table” if the parent table does
not exist.

In case you did not notice, the error you get is different from the one about a FK violation:

pysqlite2.dbapi2.IntegrityError: foreign key constraint failed

UPDATE 3

Your problem lies with an FK of spectrum_has_feature referencing a non-existent field of feature:

CREATE  TABLE IF NOT EXISTS spectrum_has_feature (
<...>
FOREIGN KEY (feature_feature_id , feature_msrun_msrun_name )
REFERENCES feature (
    feature_id , 
    msrun_msrun_msrun_name ) -- <<< shouldn't this be msrun_msrun_name?
<...>